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author ulfschaefer
date Tue, 19 Apr 2016 07:33:10 -0400
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#!/bin/bash

echo $@

BAM=$1
shift
REF=$1
shift
OUTVCF=$1

CMD="samtools mpileup -t DP,DV,DP4,DPR,SP -Auf $REF $BAM | bcftools call -m -f GQ > $OUTVCF"

echo "CMD: "$CMD
eval $CMD